Organism : Campylobacter jejuni | Module List :
Cj1617 chuD

putative haemin uptake system periplasmic haemin-binding protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog/ cog
iron ion transmembrane transporter activity go/ molecular_function
high-affinity iron ion transport go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Cj1617
(Mouseover regulator name to see its description)

Cj1617 is regulated by 3 influences and regulates 0 modules.
Regulators for Cj1617 chuD (3)
Regulator Module Operator
Cj0322 2 tf
Cj0460 2 tf
Cj0757 2 tf

Warning: Cj1617 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7386 1.30e+03 cCCcTaCTCC
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7387 6.70e+03 CTAGATTAAGTTAATAAAGG
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7676 1.80e+04 GCTTATTTaG
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7677 4.70e+03 AAGCAC
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for Cj1617

Cj1617 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type Fe3+-hydroxamate transport system, periplasmic component cog/ cog
iron ion transmembrane transporter activity go/ molecular_function
high-affinity iron ion transport go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for Cj1617

Cj1617 has total of 24 gene neighbors in modules 2, 147
Gene neighbors (24)
Gene Common Name Description Module membership
Cj0414 Cj0414 putative oxidoreductase subunit (NCBI ptt file) 2, 115
Cj0415 Cj0415 putative oxidoreductase subunit (NCBI ptt file) 2, 73
Cj0416 Cj0416 hypothetical protein Cj0416 (NCBI ptt file) 2, 156
Cj0417 Cj0417 hypothetical protein Cj0417 (NCBI ptt file) 2, 162
Cj0440c Cj0440c putative transcriptional regulator (NCBI ptt file) 90, 147
Cj0516 plsC putative 1-acyl-SN-glycerol-3-phosphate acyltransferase (NCBI ptt file) 147, 168
Cj0734c hisJ histidine-binding protein precursor (NCBI ptt file) 116, 147
Cj0755 cfrA putative iron uptake protein (NCBI ptt file) 2, 16
Cj1215 Cj1215 putative periplasmic protein (NCBI ptt file) 62, 147
Cj1380 Cj1380 putative periplasmic protein (NCBI ptt file) 103, 147
Cj1386 Cj1386 ankyrin-repeat containing protein (NCBI ptt file) 2, 40
Cj1613c Cj1613c hypothetical protein Cj1613c (NCBI ptt file) 2, 16
Cj1614 chuA haemin uptake system outer membrane receptor (NCBI ptt file) 2, 107
Cj1615 chuB putative haemin uptake system permease protein (NCBI ptt file) 2, 115
Cj1616 chuC putative haemin uptake system ATP-binding protein (NCBI ptt file) 2, 104
Cj1617 chuD putative haemin uptake system periplasmic haemin-binding protein (NCBI ptt file) 2, 147
Cjp03 tRNA-Glu tRNA-Glu (NCBI) 2, 16
Cjp25 tRNA-Ser tRNA-Ser (NCBI) 2, 16
Cjr09 Cjr09 5S ribosomal RNA (NCBI) 2, 16
Cjt2 tRNA-Asp tRNA-Asp (NCBI) 2, 16
VIMSS46110 VIMSS46110 None 2, 22
VIMSS46541 VIMSS46541 None 2, 22
VIMSS46848 VIMSS46848 None 2, 150
VIMSS47021 VIMSS47021 None 2, 73
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for Cj1617
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend